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Retold by,

Amran Md Said
Matriculation College of Pahang

1.1 Water
1.2 Carbohydrates
1.3 Lipids
1.4 Protein
1.5 Nucleic acids


At the end of this topic, students should be able to:

• explain the structure of water molecule

• describe the properties of water and its importance

Structure of a water molecule

• A water molecule consist of an oxygen atom and two hydrogen atoms

• The two hydrogen atoms are combined with the oxygen atom by sharing of electrons
• The three atoms form a triangle, not a straight line

• The water molecule is electrically neutral but there is a net negative charge on the
oxygen atom and a net positive charge on both hydrogen atoms.
• A molecule carrying such an unequal distribution of electrical charge is called a polar
• The positively charged hydrogen atoms of one water molecule are attracted to the
negatively charged oxygen atoms of nearby water molecules by forces called hydrogen

• Hydrogen bonds largely account for the unique properties of water. weaker than
covalent bonds.
• But -> strong enough to hold water molecules together.

• Because of their hydrogen bonds, water molecules are attracted to charged particles or
charged surfaces.

Properties of water as vital constituent of life

1. Water as a universal solvent

• powerful solvent for polar substances.

• These include ionic substances like sodium chloride (Na+ and Cl-), and also organic
molecules with ionized
• These cations (negatively charged ions) and anions (positively charged ions) become
surrounded by a shell of orientated water molecules.
• This makes them more reactive chemically than when they form part of an undissolve
• At the same time, non-polar substances are repelled by water, as in the case of oil on
the surface of water. Non-polar substances are hydrophobic.

2. Low viscosity of water

• This unique property makes it suitable medium of transportation in living organisms.

• Helps in movement of food substances
• It also can act as a lubricants in joints

3. High specific heat capacity


• A lot of energy is required to raise the temperature of water.

• Because, much energy is needed to break the hydrogen bonds .
• The head capacity of water is the amount of head required to raise the temperature of
1g of water by 1oC per calorie (cal) or 1 cal/g of water per oC
• This property of water is known as its high specific heat capacity.
• The specific heat capacity of water is the highest of any known substance.
• Aquatic environments like stream , lakes and seas are all very slow to change
temperature when the surrounding air temperature changes.

4. Latent heat of vaporization of water

• When pure water is heated to 100oC, it boils

• The water molecules gain sufficient kinetic energy to escape into the air as water vapor
• The heat energy that is being used to produce this change is called the latent heat of
• Water has a high latent heat of vaporization
• Because → the hydrogen bonds between water molecules make it difficult for them to
be separated and vaporized

• This means that much energy is needed to turn liquid water into water vapor.
• The amount of heat energy needed to melt ice is very high and the amount of heat that
must be removed from water to turn into ice is also great.
• Many living organism use this feature of water as cooling mechanism.
• For example, human sweat → the liquid water in sweat absorbs heat energy from the
skin or in transpiration from green leaves → to stop the leaves’ temperature from rising

too high on a hot day

5. Effect of temperature on water density

• Most liquids contract on cooling, reaching their maximum density at their freezing point.
• Water is unusually reaching its maximum density at 4ºC.
• As water freezes, the ice formed is less dense than the cold water around it. The ice
floats on top.
• The floating layer of ice insulates the water below.

• This is why the bulk of ponds, lakes or the sea rarely freeze solid.
• Aquatic life can generally survive a freeze-up.

6. High Surface Tension - adhesive and cohesive forces

• Water adheres strongly to most surfaces

• It can be drown up into long columns through narrow tubes like the xylem vessels of
plant stems, without the water column breaking.
• Compared with other liquids, water has extremely strong adhesive and cohesive
properties that prevent the column breaking under tension.
• The outermost molecules of water form hydrogen bonds with water molecules below
• This gives a very high surface tension to water- higher than that of any other liquid
except mercury. Surface skate.
• The insect’s waxy cuticle prevents wetting of its body, and the mass of the insect is not
great enough to break through the surface.


Learning Outcomes:

At the end of the lesson, student should be able to explain:

1. Describe various forms and classes
2. Describe the formation and breakdown of maltose
3. Structures and functions of starch, glycogen and cellulose.


• Organic molecule containing the element carbon, hydrogen and oxygen in a 1:2:1 ratio
• Written as (CH2O)n ; n = number of carbon

Use of carbohydrates:

• Source of energy
• Storage of energy
• Structural component of cell membranes and cell walls
• Carbohydrates can be classified into three classes:
1. monosaccharides :- single sugars
2. disaccharides :- double sugars
3. polysaccharides :- many sugars


• Physical Characteristic:
1. Small
2. White
3. Sweet

4. Soluble
5. Can be crystallized
• Chemistry Characteristic
1. reducing Benedict test
2. condensation reaction to form disaccharide or polysaccharide

• Greek words, monos = simple; sacchar = sugar, generally have molecular formula that
are some multiple of CH2O.
• - (CH2O)n For example, glucose has the formula C6H12O6.
• Most names for sugars end in -ose.
• basic unit or monomer

• It can be classified by two ways :

1. By the number of carbons in the backbone
2. By the functional group

Classification by the number of carbon in the backbone

• Three carbon (3C) – triose sugars . Example : glyseraldehyde and dihydroxyaceton

• Five carbon (5C) – pentose sugars. Example : ribose and ribulose
• Six carbon (6) – hexose sugars Example : glucose and fructose

Ring Structure for pentose

• Importance as synthesis of nucleic acid (RNA and DNA)

Ring Structure for hexose

• Importance as source of energy in cell respiration


Classification by the functional group

Example :
• Aldehyde group – glyseraldehyde, ribose and glucose
• Ketone group – dihydroxyaceton, ribulose and fructose

Functional Groups

Differences between aldehyde and ketone group

• All sugar contain the C = O. This is called a carbonyl group

• The monosaccharides which have a aldehyde group is called aldose sugar

• The monosaccharides which have ketone group is called ketose sugar

Carbonyl Groups

If the location of carbonyl group is in the middle backbone of the corbon, it call ketose

Reducing sugar

• Aldehydes are reducing agents.

• So aldose sugar have reducing agents, and are called reducing sugar.
• Ketose sugars do not have reducing agents, but in monosaccride form, it react as
reducing agents because hydroxyl in functional group have free.

Benedict’s test

• Benedict’s reagent contains copper (II) ions, which give a blue colour to the Benedict’s
• When heated with a reducing sugar, the copper (II) ions are reduced to copper (I) ions,
and an orange-red precipitate of copper (I) oxide is formed:

reducing + Cu2+ → oxidised + Cu+

sugar (oxidised) sugar (reduced)


Isomer = molecules which have same chemical formula but

with different structure
Example : glucose and fructose → C6H12O6

α and β isomers

Example : α - glucose and β - glucose

With six carbon atoms numbered.

At Carbon 1 ,
α glucose – has OH down
β glucose – has OH up


• Disaccharides are formed when two monosaccharide joined together

• Physic characteristic
- Sweet
- soluble in water.
- Can be crystallized

• Chemistry characteristic
- Reducing Benedict test (except sucrose)
• A monosaccharide able joined together to form it by a condensation reaction.
• By hydrolysis reaction to form monosaccharide.

Types of Disaccharide

• Maltose : Malt sugar, an ingredient for brewing beer, reducing sugar.

• Sucrose :Source sugar-cane, in plant (main form that is transportation in plant), non-
reducing sugar.
• Lactose :found in milk and, important energy source for young mammals, can only be
digested slowly.

Formation of disaccharide

• The two monosaccharide joined together by a condensation reactions in which water is

• The bond formed between two monosaccharide as a result of condensation is called
glycosidic bond
• A glycosidic bond can also be broken down to release separate monomer units. This
is called hydrolysis because water is needed to split up the bigger molecule
• Maltose, malt sugar → α glucose + α glucose
• Sucrose, table sugar → α glucose + α fructose .
• Lactose, milk sugar → glucose + galactose

Formation of disaccharide : Maltose


• Milk sugar, is found exclusively in milk and is an important energy source for young
• It can only be digested slowly, so gives a slow steady release of energy.
• Lactose = glucose + galactose

Formation of disaccharide : Sucrose


Reducing sugar

All monosaccharides and some disaccharide (maltose and lactose) are type of chemical
reaction knows as reduction.
Sucrose (non reducing sugar) and polysaccharide can’t reducing Benedict test.

Reducing sugar : maltose

Non reducing sugar : sucrose


• Are formed when many hundreds of monosaccharides condense (join) to form chains.
• The chains formed may be:
- Variable in length
- Branched or unbranched
- Folded – ideal for energy storage
- Straight or coiled

• Characteristic of polysaccharides:
- large,
- not sweet
- Insoluble in water
• Polysaccharides are polymers of hundreds to thousands of monosaccharides joined
by glycosidic linkages.
• Function → is as an energy storage macromolecule that is hydrolyzed as needed.
• Others → serve as building materials for the cell or whole organism.

• Starch is a storage polysaccharide in plants.
• monomers are joined by 1-4 linkages between the α glucose, known as α-1,4 glycosidic
bond .
• unbranched form of starch → amylose → forms a helix.
• Branched forms → amylopectin.

• Made from α-glucose molecules
• Forming unbranched helical chain of 300 units in length.
• Each α-glucose is joined by a glycosidic bond between neighbouring C1 and C4 atoms.


• Made from α-glucose molecules

• Forming branched chains of up to 1500 units
• Branches occur every 30 units and are formed between neighbouring C1 and C6
atoms which are then held together by glycosidic bond.




• Animals also store glucose in a polysaccharide called glycogen.

• Glycogen is highly branched, like amylopectin.
• Found in liver and muscle tissue and made up of short branched chains of α-glucose


• Major component of the tough wall of plant cells.

• Long chains of β-glucose units which are unbranched
• but parallel strands of cellulose are linked by means of hydrogen bonds, making the
cell wall a very stable structure.

• The enzymes that digest starch cannot hydrolyze the beta linkages in cellulose.
• Cellulose in our food passes through the digestive tract and is eliminated in feces as
“insoluble fiber”.
• As it travels through the digestive tract, it abrades the intestinal walls and stimulates
the secretion of mucus.
• Some microbes can digest cellulose to its glucose monomers through the use of
cellulase enzymes.
• Herbivores, like cows , have symbiotic relationships with cellulolytic microbes, allowing
them access to this rich source of energy.
• Cows do have enzymes → amylases, which can break β - 1,4 glicosidic bonds in
starch but which cannot recognize β - 1,4 glicosidic bonds in cellulose,
• the bacteria in the rumen do produce enzymes called cellulles which can recognize
and break β - 1,4 glicosidic bonds in cellulose


Retold by,

Amran Md Said
Matriculation College of Pahang


• General term for any water-insoluble organic molecules that can be extracted from
cells by ethers, benzene, or other nonpolar solvents.
• They contain carbon, hydrogen and oxygen, with far more hydrogen and carbon
compared with oxygen than in carbohydrates;
• They are insoluble in water .
• 3 major classes of lipids
1. triglycerises → e.g. Fat & oil
2. phospholipids → e.g. Lecithin
3. steroids → e.g. Cholesterol & Testosterone

Importance of lipids

• Energy storage
• Component of cell membrane
• Insulation : blubber
• Emulsifiers
• Important carriers or precursors of important flavor and odor compounds.
• Transports fat-soluble vitamins
• Immune system
• Contributes to obesity, coronary heart disease and other health problems.


• Composed of 3 fatty acid molecules attached to a glycerol backbone


• Triglycerides with reletively short fatty acid chains, or with unsaturated fatty acids, tend
to be liquid at normal temperaturated and called oils.
• Triglycerides with longer fatty acid chains, or with saturated fatty acid, are more likely
to be solid and are called fats.

• Triglycerides, like all lipids, are insoluble in water. This is because they have no dipoles
and no charges which can attract water molecules.
• Are especially useful as energy stores, because they contain much energy per gram
than either carbohydrates or proteins.

• Formation via condensation

• breakdown by hydrolysis


• Long linear hydrocarbon chains

• One end - contains a carboxylic acid group
• The other end is the methyl, "n" or omega end.

Classification of fats based on fatty acids

1. Saturated fat : saturated fatty acid → eg. Stearic acid

2. Unsaturated fat : unsaturated fatty acid → eg. oleic acid

Classification of essential

• Essential fatty acids

- Body can’t produce own fatty acids, so it’s needed from food.
• Non-essential fatty acids.
– Body can synthesise fatty acids itself


• Example : Lecithin (in cell membrane structure).


• Importance of lecithin in cell membrane structure:-

• Polarization leads to solubility in water. It act as a permeability barrier, so that

exchanges across this membrane are very limited and very slow.
• Permeable to water molecules, but not to ions such as Na +, K+, and Cl-.


Examples : Cholesterol & Testosterone.

• Structure of Steroids.


At the end of the lesson, student should be able to:

• Describe the basic structure and classes of amino acids

• Explain how amino acids are grouped
• Describe the formation and breakdown of dipeptide
• Explain structure levels of proteins and the types of bonds involved
• Explain the effect of pH and temperature on the structure of protein
• Classify of proteins according to their structure


• Protein are polymers whose molecules are made from many amino acid molecules
linked together.
• Protein consists of carbon, hydrogen, oxygen and nitrogen.
• Function of protein:
- Enzymatic catalysis .
- Transport of respiratory gases and storage.
- Structure and support
- Contacts or co-ordination (hormones)
- Immunity.
- Growth and development – membrane proteins.
- Heredity

Protein molecule

• Each different proteins molecule is made under the direction of its own gene and
performs its precise function.
• The shape of it is determined by its amino acids sequence.
• Amino acids are the building blocks from which protein are made.
• There are about 20 commonly occuring amino acids in protein.
• All have the same basic structure but differ in their RESIDUAL CHAIN ( R ).
• Amino Acid Structure

• An amino acid is a molecule containing an amino group (-NH2), a carboxyl group (-

COOH), and a hydrogen atom.

• Amino group (-NH2) has characteristics such as basic.

• Carboxyl group (-COOH) has characteristics such as acidic.
• Each amino acid has unique chemical properties determine by the nature of the side
group (indicated by R).
• For example, when the side group is –CH2OH, the amino acid (serine) is polar, but
when the side group is –CH3, amino acid (alanine) is nonpolar.
• Type of amino acid, Base on side chain group ®
- Polar → eg. Serine (Ser)
- Non polar → eg. Glycine (Gly)
- Acidic → eg. Aspartic acid (Asp)
- Basic → eg. Lysine (Lys).

Formation of Polypeptides

• Two amino acids can be joined by a condensation reaction to form a dipeptide.

• If any amino acids are joined together by peptide bonds then a polypeptide is formed.
• A polypeptide usually contains hundreds of amino acids.
• The repeated sequence (-N-C-C-N-) is the polypeptide backbone.

• amino acids are structure of protein

• The twenty commonly occurring amino acids can be arranged in an enormous variety
of different ways in giving rise to many different proteins
• A plant can synthesis all amino acids as needed from simple component.
• But an animal can’t synthesis apart of amino acids
• Base on essential, amino acids divide 2 categories
i) Essential amino acid – eg. Methionine, lysine and Valine
ii) Non-essential amino acid – eg. Glycine, alanine and Cysteine.

Structure of proteins

• A typical protein consists of one or more polypeptide chains which may be folded,
branched and cross-linked at intervals.
• Each proteins has a specific three-dimensional shape.
• In describing the structure of a protein, it is usual to refer to four separate levels of
• Primary (10), secondary (20), tertiary (30) and quaternary (40) levels of protein.

Primary structure
• This discribe the sequence of amino acids in the protein and usually determines its
eventual shape and biological function.

Secondary structure
• Once a linear chain of amino acids is formed it spontaneously folds to form α helix or β
pleated sheet.
• Hydrogen bonds holds the secondary structure together.

Tertiary structure

• Once they have been folded by hydrogen bonds, polypeptides may then fold into a
globular shape which is maintained by
- hydrogen bonds,
- ionic bonds
- disulphide bridge
Example myoglobin.

• Hydrogen bond – bond between polar side chains

• Ionic bond – bond between positively and negatively charged side chains
• disulphide bridge (covalent bonds between sulphur atoms in the residual chains of the
amino acids.)
• Hydrophobic interactions & van der Waals interactions – Nonpolar R group with
another nonpolar R group

Quaternary structure

• Consists of more than one polypeptide chains to form a single functional molecule
• Held together by hydrophobic interactions, hydrogen bonds, ionic bonds and disulfide
• Associated with non-protein groups into a large complex protein molecule

Human haemoglobin is an example.

• It consists of four chains (two α-polypeptide chains and two β-polypeptide chains)
wrapped around an iron hem group.

Effect of pH and temperature on structure of protein

• Structure of protein maintain by hydrogen bond ( 2 , 3 and 4); ionic bond, hydrophobic
interaction, disulfide bridge and van de waals interaction ( 3, 4)
• Breakage the bond causes loss of specific three-dimensional shape of a protein
• They change may be temporary or permanent

• But amino acid sequence remains unaffected

• Change shape of protein – denaturation
• Denaturation occurs under extreme conditions such as extreme pH and temperature.
• Molecule unfolds and can no longer perform its normal biological function

• If the temperature or pH exceeds a protein’s range of tolerance, its polypeptide

chains will unwind or change shape, causing to lose its conformation and hence its
ability to function

• Example: Proteins are easily damaged by heat (temperatures greater than 40 0C) due
to breakage of their cross linkages

• This cause the protein molecules to open up, straighten the folds and assume a
random configuration
• For some proteins, denaturation might be reserved when normal conditions are
• Classifation base on structure
• Divided by 3 classification base on structure.
- Conjugated protein
- Globular protein
- Fibrous protein

Conjugated Protein

• protein joined with non protein component/ prosthetic group

• Protein structure merge with with non protein group (prosthetic group)
• Eg. Haemoglobin contains the prosthetic group containing iron, which is the haem. It is
with in the haem group that carries the oxygen molecule through the binding of the
oxygen molecule to the iron ion (Fe 2+) found in the haem group

Globular Protein

• Mostly, that protein related in tertiary and quaternary structure.

• Usually water soluble (can to form colloid)
• Long polypeptide with helix to form globular or spherical
• example: globulin (blood serum), enzymes, antibody, hormone

Fibrous Protein

• Mostly, that protein related in secondary structure.

• Insoluble in water and very strong because its make from long polypeptide
• example: collagen, myosin, fibrin and keratin

Differences between fibrous protein and globular proteins

Properties of protein

• Amphoteric
• Buffering capacity
• Colloidal properties
• Denaturation

Note :
Properties of Protein, just for extra knowledge

Properties of protein

1. Amphoteric

• In aqueous as neutral (pH 7), amino acid such as dipole, its called zwitterions
• Amphoteric because have characteristic both acidic and basic.

• In aqueous acidic (< pH 7), protein receive H+ and make its positive charge.
• In aqueous alkaline (>pH 7), donate H+ and make its negative charge.
• Charge at zwitterions depend on pH
• pH at amino acid as neutral like electric its call isoelectric
• All amino acids have own characteristic as isoelectric point (pI).

2. Buffering capacity

• Amphoteric characteristic of amino acids, its make such as buffer

• A buffer solution is one which resist the tendency to alter its pH even when small
amounts of acid or alkali are added to.
• That mean a buffer solution can’t change spontaneously, while added pH increase
(basic) . Amino acids will donate hydrogen ionic.
• While pH reduce (acidic), amino acids will receive hydrogen ionic.

3. Colloidal properties

4. Denaturation

• The structure of a protein can be change if the bonds which hold it in shape are
broken. This process is called Denaturation.
• High temperatures break hydrogen bond and van der Waals forces. In a globular
protein a long chain instead of a curled-up ball. The molecules will no longer be soluble
in water.
• Extremes of pH break ionic bond, because they alter the charges on R groups.
• Reducing agents break disulphide bond. This is made use of when perming hair.
Keratin, from which hair is made, contains disulphide bond that hold the shape in


Topic distinguish

At the end of the lesson, students should be able to:

• Describe the structure of nucleotide as the basic composition of nucleic acid (DNA and
• Describe the structure of DNA based on the Watson and Crick Model.
• State the type and function of RNA
• State the differences of DNA and RNA

Nucleic acids
• The amino acid sequence of a polypeptide is programmed by a gene.
• A gene consists of regions of DNA, a polymer of nucleic acids.
• DNA (and their genes) is passed by the mechanisms of inheritance.

Structure of nucleotide

• Nucleic acids are polymers of monomers called nucleotides.

• Each nucleotide consists of three smaller molecules. These are :
1. A phosphate group
2. A pentose sugar
3. A nitrogenous base

Phosphate group

Pentose sugar

Nitrogenous base

• 3 components are combined by CONDENSATION reaction.

• 3 components are breakdown by HYDROLYSIS reaction.


• Double stranded polymer of nucleotides

• Contains 4 bases (not include uracil (U) ):
i.Adenine (A)
ii.Guanine (G)
iii.Cytosine (C)
iv.Thymine (T)
• Long and thin strand
• Amount between A and T and G and C usually equal to each other because A always
pairing with T and G with C
• Helix shape is maintained by HYDROGEN BONDS

• James Watson and Francis Crick postulated double helix of 2 nucleotides strands
• Nucleotide strands being linked together by pairs of nitrogenous bases which are
joined by hydrogen bonds
• Purines ; double ring structures form longer links if paired together than pyrimidide
• Only by pairing 1 purine with 1 pyrimidine – consistent separation of 3 rings’ width can
be achieved
• Deoxyribose and phosphate units form the uprights while nitrogenous base pairings
form the rungs
• 2 chains that form the uprights run in opposite direction (antiparallel)


• Single stranded polymer of nucleotides

• Pentose sugar – ribose
• Organic bases – Guanine, Cytosine, Adenine and Uracil (replacing thymine)
• 3 types of RNA :
i.Messenger RNA (mRNA)
ii.Transfer RNA (tRNA)
iii.Ribosomal RNA (rRNA)


• Large,complex molecule
• Made up of double and single helix
• Manufactured by DNA of the nucleus
• Found in ribosome
• Comprises of more than half the mass of the total RNA of the cell
• The Base sequence is similar in all organisms


• Small molecule, comprising single strand

• Manufactured by nuclear DNA
• Made up 10 -15 % of cell’s RNA
• All type are fundamentally similar
• Form clover-leaf shape, one end of the chain ending with C-C-A sequence
• Which amino acid attaches itself
• ≥ 20 types of tRNA, carrying different amino acid

• At an intermediate point along the chain is an important sequence of 3 bases –



• Long stranded molecule, up to thousands of nucleotides form into helix

• Manufactured in nucleus
• Mirror copy of a part of a strand of DNA
• There is hence an immense variety of types
• Enter the cytoplasm – associate with ribosomes and acts as template for protein
• Made up less than 5% of total cellular RNA
• Easily and quickly broken down, sometimes existing for only a matter of minutes.

Edited on Mei, 31 2011

Retold by,

Amran Md Said
Matriculation College of Pahang

– The End -